Transformer

CATs: Semantic Correspondence with Transformers

CATs Semantic Correspondence with Transformers Our model CATs is illustrated below: git clone https://github.com/SunghwanHong/CATs cd CATs conda create -n CATs python=3.6 conda activate CATs pip install torch==1.8.0+cu111 torchvision==0.9.0+cu111 torchaudio==0.8.0 -f https://download.pytorch.org/whl/torch_stable.html pip install -U scikit-image pip install git+https://github.com/albumentations-team/albumentations pip install tensorboardX termcolor timm tqdm requests pandas Download pre-trained weights on Link All datasets are automatically downloaded into directory specified by argument datapath Result on SPair-71k: (PCK 49.9%) python test.py –pretrained “/path_to_pretrained_model/spair” –benchmark spair Result on SPair-71k, feature backbone frozen: (PCK […]

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Security

Headless chatbot that detects spam and posts links to it to chatrooms for quick deletion

SmokeDetector Headless chatbot that detects spam and posts it to chatrooms. Uses ChatExchange, takes questions from the Stack Exchange realtime tab, and accesses answers via the Stack Exchange API. Basic setup To set up SmokeDetector, please use git clone https://github.com/Charcoal-SE/SmokeDetector.git cd SmokeDetector git checkout deploy sudo pip3 install -r requirements.txt –upgrade pip3 install –user -r user_requirements.txt –upgrade Next, copy config.sample to a new file called config,and edit the values required. To run, use python3 nocrash.py(preferably in a daemon-able mode, like […]

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Monitoring

Real-time Coastal Monitoring at the University of Hawaii at Manoa

Coastal Monitoring at the University of Manoa Source code for Beaglebone/RPi-based data loggers, shore internet gateways, and web server. Software developed for the Coastal Environment Monitoring project at the University of Hawaii at Manoa. Project website: https://grogdata.soest.hawaii.edu/project_info/ I’m using this mostly for synchronizing the software and configurations on our gateways, loggers, and servers; I’m not using this to track issues or updates. More like “Dropbox for source code” than “git for source control”. That said, the drivers/ folder does contain […]

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Tool

MDAnalysis tool to calculate membrane curvature

Membrane Curvature This is an MDAnalysis module to calculate membrane curvature from molecular dynamics simulations. The MDAkit for membrane curvature analysis is part of the Google Summer of Code program and it is linked to a Code of Conduct. Abstract Elements of differential geometry enable us to quantify the curvature of a surface. The core elements of biological membranes, phospholipids, provide tridimensional configurations from which a surface can be derived to calculate curvature descriptors. We would like to integrate to […]

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Data Analysis

A Python library to analyze molecular dynamics trajectories

MDAnalysis MDAnalysis is a Python library for the analysis of computer simulations of many-body systems at the molecular scale, spanning use cases from interactions of drugs with proteins to novel materials. It is widely used in the scientific community and is written by scientists for scientists. It works with a wide range of popular simulation packages including Gromacs, Amber, NAMD, CHARMM, DL_Poly, HooMD, LAMMPS and many others — see the lists of supported trajectory formats and topology formats. MDAnalysis also […]

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Maps

Solving the Traveling Salesman Problem using Self-Organizing Maps with python

som-tsp Solving the Traveling Salesman Problem using Self-Organizing Maps This repository contains an implementation of a Self Organizing Map that can be used to find sub-optimal solutions for the Traveling Salesman Problem. The instances of the problems that the program supports are .tsp files, which is a widespread format in this problem. All the source code can be found in the src directory, while a report and brief presentation slides (in Spanish) can be found in the report folder. To […]

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Monitoring

A python module for monitoring memory consumption

Memory Profiler This is a python module for monitoring memory consumption of a process as well as line-by-line analysis of memory consumption for python programs. It is a pure python module which depends on the psutil module. Installation Install via pip: $ pip install -U memory_profiler The package is also available on conda-forge. To install from source, download the package, extract and type: $ python setup.py install Usage line-by-line memory usage The line-by-line memory usage mode is used much in […]

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Natural Language Processing

Super easy library for BERT based NLP models with python

Fast-Bert Supports LAMB optimizer for faster training. Please refer to https://arxiv.org/abs/1904.00962 for the paper on LAMB optimizer. Supports BERT and XLNet for both Multi-Class and Multi-Label text classification. Fast-Bert is the deep learning library that allows developers and data scientists to train and deploy BERT and XLNet based models for natural language processing tasks beginning with Text Classification. The work on FastBert is built on solid foundations provided by the excellent Hugging Face BERT PyTorch library and is inspired by […]

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Hardware

A Python package that generates hardware pinout diagrams as SVG images

pinout SVG diagram creation from Python code – pinout provides an easy method of creating pin-out diagrams for electronic hardware. Please visit pinout.readthedocs.io for the full quick start tutorial and detailed documentation on all options provided by the pinout package. Quick start pinout can be easily installed with pip and provides some sample files that demonstrate key features. Install Using a virtual environment is recommended; Start by installing the pinout package. Either clone this repo and pip install it or […]

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Data Analysis

X-ray Analysis for Synchrotron Applications using Python

Larch Larch is an open-source library and set of applications for processing and analyzing X-ray absorption and fluorescence spectroscopy data and X-ray fluorescence and diffraction image data from synchrotron beamlines. It is especially focussed on X-ray absorption fine-structure spectroscopy (XAFS) including X-ray absorption near-edge spectroscopy (XANES) and extended X-ray absorption fine-structure spectroscopy (EXAFS). It also supports visualization and analysis tools for X-ray fluorescence (XRF) spectra and XRF and X-ray diffraction (XRD) images as collected at scanning X-ray microprobe beamlines. Larch […]

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